My top five would be...
Rugrats - one of the few cartoons that actually spawned excellent movies as well
The Powerpuff Girls - for gifting us with "Him", the character that turned everyone queer
Scooby Doo, Where Are You? - "What's New?" was good too, and again it spawned some good movies (I think they're making a new one too?) and has hugely influenced pop culture.
Animaniacs - for the greatest theme tune of all time (and also because it contains Pinky and the Brain, too)
The Simpsons - almost forgot to include this one because it was so much more than "a cartoon". One of the best shows of all time, until it decided not to be.
Close mentions: Tom and Jerry, Hey Arnold and Fairly Odd Parents. Classic American Dad, too.